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Published on: July 22, 2020
Precision Medicine Gene Network Analyser: part I-cancer driver gene identification through network topology and
Rashmi Siddalingappa1, Showket Hussain2, Deepa S3
1Department of Computer and Data Science, York St John University, London, UK. r.siddalingappa@yorksj.ac.uk.
Purpose:
Precision oncology depends on identifying cancer driver genes and linking them to targeted therapies. Current methods using curated gene sets or generic classifiers often miss biologically relevant patterns in complex gene interaction networks.
Methods:
We developed the Precision Medicine Gene Network Analyser, integrating network topology analysis with machine learning for cancer gene identification. The dataset included 699 cancer driver genes (COSMIC Cancer Gene Census) and 15,050 background genes, mapped to high-confidence protein-protein interaction networks from STRING (456,300 edges, 15,749 nodes). Network features such as degree, betweenness, PageRank, k-core, and clustering coefficients were extracted. Imbalance Aware Network Integrator (IANI) was proposed to address class imbalance, where balanced resampling and ensemble models (logistic regression, random forest, gradient boosting) were combined with deep neural networks using focal loss, optimising thresholds for maximum F1-score. Hub genes were defined using a statistical cutoff of mean outdegree + 2 × SD (standard deviation).
Results:
On a test set of 3150 samples (140 cancer, 3010 non-cancer genes), the optimised ensemble improved ROC-AUC from 0.84 to 0.96, precision from 0.78 to 0.90, and recall from 0.42 to 0.81 (F1 = 0.85) at a threshold of 0.466. Hub analysis identified 689 hubs with fourfold enrichment of cancer genes (16.1% vs. 4.4%, p < 10 - 20), showing higher betweenness centrality (p < 0.001). Key features such as degree (0.32), betweenness (0.24), and PageRank (0.19) contributed 75% of the model's performance. Top hubs (TP53: 758, EGFR: 512, AKT1: 415 connections) showed 60-67% cancer gene enrichment, with pathway clustering in p53 signalling (75%) and cell cycle regulation (67.7%).
Conclusion:
Integrating protein interaction topology with imbalance-aware machine learning achieved 96% discrimination accuracy. This work forms a base for the upcoming phases of drug-gene mapping and patient-specific therapy prediction within the Precision Medicine Gene Network Analyser.
Insights
This study introduces a novel network analysis tool for precision oncology, improving cancer gene identification accuracy to 96%. The Precision Medicine Gene Network Analyser integrates network topology and machine learning to identify key cancer driver genes for targeted therapies.
Area of Science:
- Bioinformatics
- Computational Biology
- Genomics
Background:
- Precision oncology requires accurate identification of cancer driver genes for targeted therapy development.
- Existing methods often fail to capture complex patterns within gene interaction networks.
Purpose of the Study:
- To develop an integrated network analysis and machine learning approach for enhanced cancer gene identification.
- To improve the accuracy of distinguishing cancer genes from background genes using network topology and machine learning.
Main Methods:
- Developed the Precision Medicine Gene Network Analyser, combining network topology (degree, betweenness, PageRank) with machine learning.
- Utilized protein-protein interaction networks (STRING) and COSMIC cancer gene data.
- Proposed the Imbalance Aware Network Integrator (IANI) to handle class imbalance, employing ensemble models and deep neural networks with focal loss.
Main Results:
- Achieved 96% discrimination accuracy, significantly improving ROC-AUC (0.96), precision (0.90), and recall (0.81).
- Identified 689 hub genes with a fourfold enrichment of cancer genes (16.1% vs. 4.4%, p < 10^-20).
- Key network features (degree, betweenness, PageRank) contributed 75% to model performance; top hubs like TP53 and EGFR showed high cancer gene enrichment.
Conclusions:
- Integrating protein interaction network topology with imbalance-aware machine learning provides high accuracy for cancer gene identification.
- The Precision Medicine Gene Network Analyser serves as a foundation for future drug-gene mapping and personalized therapy prediction.
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